Revealing evolutionary constraints on proteins through sequence analysis

Principles for Optimal Cooperativity in Allosteric Materials

(2018) Le Yan et al.   BIOPHYSICAL JOURNAL

Power law tails in phylogenetic systems

(2018) Chongli Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Green function of correlated genes in a minimal mechanical model of protein evolution

(2018) Sandipan Dutta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolution-based inference of amino acid interactions underlying protein function

(2018) Victor H Salinas et al.   eLife

Inferring the shape of global epistasis

(2018) Jakub Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selection for Protein Stability Enriches for Epistatic Interactions

(2018) Anna Posfai et al.   Genes

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Patterns of coevolving amino acids unveil structural and dynamical domains

(2017) Daniele Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Designing allostery-inspired response in mechanical networks

(2017) Jason W. Rocks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupling between Protein Stability and Catalytic Activity Determines Pathogenicity of G6PD Variants

(2017) Anna D. Cunningham et al.   Cell Reports

Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

(2016) R. R. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring interaction partners from protein sequences

(2016) Anne-Florence Bitbol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis

(2016) Thomas Gueudré et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable

(2016) John P. Barton et al.   Nature Communications

Evolution-Based Functional Decomposition of Proteins

(2016) Olivier Rivoire et al.   PLoS Computational Biology

Evolutionary Conserved Positions Define Protein Conformational Diversity

(2016) Tadeo E. Saldaño et al.   PLoS Computational Biology

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

(2015) Duccio Malinverni et al.   PLoS Computational Biology

Protein Sectors: Statistical Coupling Analysis versus Conservation

(2015) Tiberiu Teşileanu et al.   PLoS Computational Biology

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

(2014) Ryan R. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

(2014) Jaclyn K. Mann et al.   PLoS Computational Biology

Predicting Functionally Informative Mutations in Escherichia coli BamA Using Evolutionary Covariance Analysis

(2013) R. S. Dwyer et al.   GENETICS

Elements of Coevolution in Biological Sequences

(2013) Olivier Rivoire   PHYSICAL REVIEW LETTERS

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

(2013) Simona Cocco et al.   PLoS Computational Biology

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

High-dimensional inference with the generalized Hopfield model: Principal component analysis and corrections

(2011) S. Cocco et al.   PHYSICAL REVIEW E

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

(2011) V. Dahirel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A biophysical protein folding model accounts for most mutational fitness effects in viruses

(2011) C. S. Wylie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

A network of dynamically conserved residues deciphers the motions of maltose transporter

(2009) Suryani Lukman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA